+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10427 | ||||||||||||
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Title | Structure of the five-fold capsomer of the dArc2 capsid | ||||||||||||
Map data | dArc2 five-fold capsomer | ||||||||||||
Sample |
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Function / homology | Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / extracellular vesicle / RNA binding / membrane / identical protein binding / Activity-regulated cytoskeleton associated protein 2 Function and homology information | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Erlendsson S / Morado DR / Shepherd JD / Briggs JAG | ||||||||||||
Funding support | Denmark, United States, United Kingdom, 3 items
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Citation | Journal: Nat Neurosci / Year: 2020 Title: Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins. Authors: Simon Erlendsson / Dustin R Morado / Harrison B Cullen / Cedric Feschotte / Jason D Shepherd / John A G Briggs / Abstract: Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high- ...Arc, a neuronal gene that is critical for synaptic plasticity, originated through the domestication of retrotransposon Gag genes and mediates intercellular messenger RNA transfer. We report high-resolution structures of retrovirus-like capsids formed by Drosophila dArc1 and dArc2 that have surface spikes and putative internal RNA-binding domains. These data demonstrate that virus-like capsid-forming properties of Arc are evolutionarily conserved and provide a structural basis for understanding their function in intercellular communication. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10427.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-10427-v30.xml emd-10427.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_10427.png | 78.8 KB | ||
Others | emd_10427_additional.map.gz | 9.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10427 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10427 | HTTPS FTP |
-Related structure data
Related structure data | 6tatMC 6tapC 6taqC 6tarC 6tasC 6tauC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10427.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dArc2 five-fold capsomer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.388 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: dArc2 five-fold capsomer unsharpened
File | emd_10427_additional.map | ||||||||||||
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Annotation | dArc2 five-fold capsomer unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dArc2 Capsids
Entire | Name: dArc2 Capsids |
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Components |
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-Supramolecule #1: dArc2 Capsids
Supramolecule | Name: dArc2 Capsids / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all Details: The five-fold dArc2 capsomer map is generated by symmetry expansion, sub-boxing and local refinement. |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Activity-regulated cytoskeleton associated protein 2
Macromolecule | Name: Activity-regulated cytoskeleton associated protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 22.656734 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE ...String: MTQMSDEQFR IFIETIKSLG PIKEEPPSKG SFSNCTVRFS GQRDHDAVDE FINAVETYKE VEGISDKDAL KGLPLLFKSI AVVWWKGVR RDAKTWSDAL QLLRDHFSPT KPSYQIYMEI FETKQSYDEV IDSFICKQRA LLAKLPEGRH DEETELDFIY G LMQPKYRE SIPRHEVKTF RELLDRGRTV ERTRH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | dArc2 capsids |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-75 / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 21348 Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units ...Details: From 1779 initial dArc2 icosahedral capsids, we performed symmetry expansion as implemented in RELION, to calculate the positions and orientations for each of the 106,740 asymmetric units for dArc2, centered at the five-fold capsomeres. We extracted individual capsomeres using a box size of 148 pixels. For the five-fold capsomeres we removed the redundant five-fold symmetrized capsomeres leaving 21,348 particles. | ||||||
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CTF correction | Software:
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 21348 |